Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Community of Bark and Ambrosia Beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) in Agricultural and Forest Ecosystems with Laurel Wilt

Redbay ambrosia beetle, Xyleborus glabratus, is an invasive wood-boring pest first detected in the USA in 2002 in Georgia. The beetle&rsquo;s dominant fungal symbiont, Harringtonialauricola, causes laurel wilt, a lethal disease of trees in the Lauraceae. Over the past 20 years, X. glabratus and laurel wilt have spread to twelve southeastern states, resulting in high mortality of native Persea species, including redbay (P. borbonia), swampbay (P. palustris), and silkbay (P. humilis). Laurel wilt also threatens avocado (P. americana) in south Florida, but in contrast to the situation in forests, X. glabratus is detected at very low levels in affected groves. Moreover, other species of ambrosia beetle have acquired H. lauricola and now function as secondary vectors. To better understand the beetle communities in different ecosystems exhibiting laurel wilt, parallel field tests were conducted in an avocado grove in Miami-Dade County and a swampbay forest in Highlands County, FL. Sampling utilized ethanol lures (the best general attractant for ambrosia beetles) and essential oil lures (the best attractants for X. glabratus), alone and in combination, resulting in detection of 20 species. This study documents host-related differences in beetle diversity and population levels, and species-specific differences in chemical ecology, as reflected in efficacy of lures and lure combinations

Data from: Attraction, oviposition and larval survival of the fungus gnat, Lycoriella ingenua, on fungal species isolated from adults, larvae, and mushroom compost

We previously showed that the females of the mushroom sciarid, Lycoriella ingenua (Dufour, 1839) (Diptera: Sciaridae), one of the most severe pests of the cultivated white button mushroom, Agaricus bisporus (J.E. Lange) Emil J. Imbach (Agaricales: Agaricaceae), are attracted to the mushroom compost that mushrooms are grown on and not to the mushrooms themselves. We also showed that females are attracted to the parasitic green mold, Trichoderma aggressivum. In an attempt to identify what is in the mushroom compost that attracts female L. ingenua, we isolated several species of fungi from adult males and females, third instar larvae, and mushroom compost itself. We then analyzed the attraction of females to these substrates using a static-flow two choice olfactometer, as well as their oviposition tendencies in another type of assay under choice and no-choice conditions. We also assessed the survival of larvae to adulthood when first instar larvae were placed on each of the isolated fungal species. We found that female flies were attracted most to the mycoparasitic green mold, T. aggressivum, to Penicilium citrinum isolated from adult female bodies, and to Scatylidium thermophilium isolated from the mushroom compost. Gravid female flies laid the most eggs on T. aggressivum, Aspergillus flavus isolated from third instar larval frass, Aspergillus fumigatus isolated from adult male bodies, and on P. citrinum. This egg-laying trend remained consistent under no-choice conditions as females aged. First instar larvae developed to adulthood only on S. thermophilium and Chaetomium sp. isolated from mushroom compost, and on P. citrinum. Our results indicate that the volatiles from a suite of different fungal species act in tandem in the natural setting of mushroom compost, with some first attracting gravid female flies and then others causing them to oviposit. The ecological context of these findings is important for creating an optimal strategy for using possible semiochemicals isolated from these fungal species to better monitor and control this pestiferous mushroom fly species

Attraction, Oviposition and Larval Survival of the Fungus Gnat, Lycoriella ingenua, on Fungal Species Isolated from Adults, Larvae, and Mushroom Compost.

We previously showed that the females of the mushroom sciarid, Lycoriella ingenua (Dufour, 1839) (Diptera: Sciaridae), one of the most severe pests of the cultivated white button mushroom, Agaricus bisporus (J.E. Lange) Emil J. Imbach (Agaricales: Agaricaceae), are attracted to the mushroom compost that mushrooms are grown on and not to the mushrooms themselves. We also showed that females are attracted to the parasitic green mold, Trichoderma aggressivum. In an attempt to identify what is in the mushroom compost that attracts female L. ingenua, we isolated several species of fungi from adult males and females, third instar larvae, and mushroom compost itself. We then analyzed the attraction of females to these substrates using a static-flow two choice olfactometer, as well as their oviposition tendencies in another type of assay under choice and no-choice conditions. We also assessed the survival of larvae to adulthood when first instar larvae were placed on each of the isolated fungal species. We found that female flies were attracted most to the mycoparasitic green mold, T. aggressivum, to Penicilium citrinum isolated from adult female bodies, and to Scatylidium thermophilium isolated from the mushroom compost. Gravid female flies laid the most eggs on T. aggressivum, Aspergillus flavus isolated from third instar larval frass, Aspergillus fumigatus isolated from adult male bodies, and on P. citrinum. This egg-laying trend remained consistent under no-choice conditions as females aged. First instar larvae developed to adulthood only on S. thermophilium and Chaetomium sp. isolated from mushroom compost, and on P. citrinum. Our results indicate that the volatiles from a suite of different fungal species act in tandem in the natural setting of mushroom compost, with some first attracting gravid female flies and then others causing them to oviposit. The ecological context of these findings is important for creating an optimal strategy for using possible semiochemicals isolated from these fungal species to better monitor and control this pestiferous mushroom fly species

Piperitone (<i>p</i>-Menth-1-En-3-One): A New Repellent for Tea Shot Hole Borer (Coleoptera: Curculionidae) in Florida Avocado Groves

The tea shot hole borer, Euwallacea perbrevis, has been recently established in Florida, USA, where it vectors fungal pathogens that cause Fusarium dieback in avocado. Pest monitoring uses a two-component lure containing quercivorol and α-copaene. Incorporation of a repellent into IPM programs may reduce the incidence of dieback in avocado groves, particularly if combined with lures in a push–pull system. This study evaluated piperitone and α-farnesene as potential repellents for E. perbrevis, comparing their efficacy to that of verbenone. Replicate 12-week field tests were conducted in commercial avocado groves. Each test compared beetle captures in traps baited with two-component lures versus captures in traps containing lures plus repellent. To complement field trials, Super-Q collections followed by GC analyses were performed to quantify emissions from repellent dispensers field-aged for 12 weeks. Electroantennography (EAG) was also used to measure beetle olfactory response to each repellent. Results indicated that α-farnesene was ineffective; however, piperitone and verbenone were comparable in repellency, achieving 50–70% reduction in captures, with longevity of 10–12 weeks. EAG responses to piperitone and verbenone were equivalent, and significantly greater than response to α-farnesene. Since piperitone is less expensive than verbenone, this study identifies a potential new E. perbrevis repellent

Two-choice attraction assays.

<p>Mean number (± SEM) of two-day-old gravid female <i>Lycoriella ingenua</i> flies attracted to various pure fungal cultures grown on potato dextrose agar in two-choice, static-flow olfactometer assays. Each horizontal bar is the mean of responses of 5 females to each treatment over 12 replicates (N = 12). The mean number of non-responders (± SEM) for each combination is included in parentheses to the right. Female choices for each pair of cultures were analyzed via chi square. All non-responders were excluded from the analysis.</p

Two-choice oviposition assays.

<p>Mean number (± SEM) of eggs laid by two-day old gravid female <i>L</i>. <i>ingenua</i> flies on various pure fungal cultures grown on potato dextrose agar in two-choice oviposition assays. Each horizontal bar shows the mean number of eggs laid on the two choices of fungi by 15 two-day-old gravid female flies, tested in groups of three in three individual chambers with 5 different cohorts of females being tested over 5 different nights. All data were non-normally distributed and differences between the mean number of eggs deposited on each pair of fungal cultures were analyzed via the Mann–Whitney <i>U</i> test (two-tailed, df = 14).</p

No-choice oviposition assays.

<p>Mean number (± SEM) of eggs laid by 0- (day of emergence) to-7 day-old female <i>L</i>. <i>ingenua</i> flies on various pure fungal cultures grown on potato dextrose agar in no-choice oviposition assays. A total of 15 flies of a particular age were tested for their tendency to lay eggs on each of the 8 fungal cultures under no-choice conditions, resulting in a total of 120 females (15 flies x 8 fungal cultures) of each age that were tested for oviposition on all fungal cultures. There were 8 age groups tested (panels a-h), and thus 840 different female flies were used in this experiment. All data were non-normally distributed and differences among mean egg numbers within each age group were analyzed via the Kruskal-Wallis test. Differences between mean egg numbers for each age group were compared using the Dunn’s Multiple Comparisons Test. No comparisons were made between mean numbers of eggs in different age groups. Different letters above histograms within the same age group indicate a significant difference (df = 14; P < 0.05).</p

Larval survival assays.

<p>Mean survival (± SEM) of <i>Lycoriella ingenua</i> larvae to adults on various pure fungal cultures grown on potato dextrose agar. Each histogram is the mean survival of 5 newly emerged first instar larvae, replicated from 6 different cohorts of larvae. All data were non-normally distributed and differences among mean survival on different fungal cultures were first analyzed via the Kruskal-Wallis test. Differences between survival on different fungal cultures were compared with the Dunn’s Multiple Comparisons Test. Different letters above bars indicate a significant difference (df = 5; P < 0.05).</p